sbmlutils.layout

Package for SBML layout.

Submodules

Package Contents

Classes

Layout

Layout.

SpeciesGlyph

SpeciesGlyph.

ReactionGlyph

ReactionGlyph.

CompartmentGlyph

CompartmentGlyph.

Attributes

LAYOUT_VERSION

LAYOUT_ROLE_SUBSTRATE

LAYOUT_ROLE_PRODUCT

LAYOUT_ROLE_SIDESUBSTRATE

LAYOUT_ROLE_SIDEPRODUCT

LAYOUT_ROLE_MODIFIER

LAYOUT_ROLE_ACTIVATOR

LAYOUT_ROLE_INHIBITOR

LAYOUT_ROLE_UNDEFINED

sbmlutils.layout.LAYOUT_VERSION = 1[source]
sbmlutils.layout.LAYOUT_ROLE_SUBSTRATE = substrate[source]
sbmlutils.layout.LAYOUT_ROLE_PRODUCT = product[source]
sbmlutils.layout.LAYOUT_ROLE_SIDESUBSTRATE = sidesubstrate[source]
sbmlutils.layout.LAYOUT_ROLE_SIDEPRODUCT = sideproduct[source]
sbmlutils.layout.LAYOUT_ROLE_MODIFIER = modifier[source]
sbmlutils.layout.LAYOUT_ROLE_ACTIVATOR = activator[source]
sbmlutils.layout.LAYOUT_ROLE_INHIBITOR = inhibitor[source]
sbmlutils.layout.LAYOUT_ROLE_UNDEFINED = undefined[source]
class sbmlutils.layout.Layout(sid, width, height, compartment_glyphs=None, species_glyphs=None, reaction_glyphs=None, depth=0, name=None, sboTerm=None, metaId=None)[source]

Bases: sbmlutils.factory.Sbase

Layout.

Parameters

  • sid (str) –

  • width (float) –

  • height (float) –

  • compartment_glyphs (Optional[List[CompartmentGlyph]]) –

  • species_glyphs (Optional[List[SpeciesGlyph]]) –

  • reaction_glyphs (Optional[List[ReactionGlyph]]) –

  • depth (int) –

  • name (Optional[str]) –

  • sboTerm (Optional[str]) –

  • metaId (Optional[str]) –

create_sbml(model)

Create SBML in model.

Parameters

model (libsbml.Model) –

Return type

libsbml.Layout

_set_fields(sbase, model)
Parameters

  • sbase (libsbml.Layout) –

  • model (libsbml.Model) –

Return type

None

class sbmlutils.layout.SpeciesGlyph(sid, species, x, y, z=0, w=50, h=20, d=0, text=None, name=None, sboTerm=None, metaId=None)[source]

Bases: sbmlutils.factory.Sbase

SpeciesGlyph.

Parameters

  • sid (str) –

  • species (str) –

  • x (float) –

  • y (float) –

  • z (float) –

  • w (float) –

  • h (float) –

  • d (float) –

  • text (Optional[str]) –

  • name (Optional[str]) –

  • sboTerm (Optional[str]) –

  • metaId (Optional[str]) –

_set_glyph_fields(obj, layout, model)

Set fields.

Parameters

  • obj (libsbml.SpeciesGlyph) –

  • layout (libsbml.Layout) –

  • model (libsbml.Model) –

Return type

None

class sbmlutils.layout.ReactionGlyph(sid, reaction, x, y, z=0, species_glyphs=None, w=20, h=20, d=0, text=None, name=None, sboTerm=None, metaId=None)[source]

Bases: sbmlutils.factory.Sbase

ReactionGlyph.

Parameters

  • sid (str) –

  • reaction (str) –

  • x (float) –

  • y (float) –

  • z (float) –

  • species_glyphs (Optional[Dict[str, str]]) –

  • w (float) –

  • h (float) –

  • d (float) –

  • text (Optional[str]) –

  • name (Optional[str]) –

  • sboTerm (Optional[str]) –

  • metaId (Optional[str]) –

_set_glyph_fields(obj, layout, model)
Parameters

  • obj (libsbml.ReactionGlyph) –

  • layout (libsbml.Layout) –

  • model (libsbml.Model) –

Return type

None

_create_curve(layout, srg, r_glyph_id, s_glyph_id, role, direction)

Heuristic for creating the curves.

Parameters

  • layout (libsbml.Layout) –

  • srg (libsbml.SpeciesReferenceGlyph) –

  • r_glyph_id (str) –

  • s_glyph_id (str) –

  • role (str) –

  • direction (str) –

Returns

Return type

None

class sbmlutils.layout.CompartmentGlyph(sid, compartment, x, y, z=0, w=200, h=200, d=0, text=None, name=None, sboTerm=None, metaId=None)[source]

Bases: sbmlutils.factory.Sbase

CompartmentGlyph.

Parameters

  • sid (str) –

  • compartment (str) –

  • x (float) –

  • y (float) –

  • z (float) –

  • w (float) –

  • h (float) –

  • d (float) –

  • text (Optional[str]) –

  • name (Optional[str]) –

  • sboTerm (Optional[str]) –

  • metaId (Optional[str]) –

_set_glyph_fields(obj, layout, model)

Set fields.

Parameters

  • obj (libsbml.SpeciesGlyph) –

  • layout (libsbml.Layout) –

  • model (libsbml.Model) –

Return type

None